SAXSdb — 8r6u

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8r6u
沉积日期 deposition_date	2023-11-23
结构标题 title	Structure of the SFTSV L protein in a transcription-priming state without capped RNA [TRANSCRIPTION-PRIMING (in vitro)]
关键词 keywords	SFTSV, RNA-DEPENDENT RNA POLYMERASE, VIRAL RNA, VIRAL PROTEIN; VIRAL PROTEIN
实验方法 method	ELECTRON MICROSCOPY

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	36.61 Å
回转半径 Rg (电子) rg_electron	35.69 Å
零角强度 I(0) i0	609150000.00
分子量 molecular_weight	191290.0 kDa
排除体积 excluded_volume	235680 Å³
包络体积 envelope_volume	312500 Å³
水化壳体积 shell_volume	69321 Å³
包络直径 envelope_diameter	120.9 Å
壳层 Rg shell_rg	44.62 Å
包络 Rg envelope_rg	35.16 Å
形状 Rg shape_rg	35.69 Å
总 Rg total_rg	36.26 Å
总原子数 total_atoms	13392
残基数 n_residues	1609
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	109.6 Å
Rg (实空间) rg_real	36.38 Å
Rg 误差 (实空间) rg_real_error	0.54 Å
I(0) (实空间) i0_real	6.0910e+08
I(0) 误差 (实空间) i0_real_error	9.5690e+06
Rg (倒空间) rg_reciprocal	36.53 Å
I(0) (倒空间) i0_reciprocal	609200000.0000
解质量估计 total_estimate	0.6684
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	45.9 Å
偏度 Skewness skewness	0.166
峰度 Kurtosis kurtosis	-0.399
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	119400000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 0.048; Positv: 1.000; Valcen: 0.971; Smooth: 0.754

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	RNA-directed RNA polymerase L
分子量 formula_weight	235698.5 kDa
突变 mutation	D112A
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	13408

MNLEVLCGRINVENGLSLGEPGLYDQIYDRPGLPDLDVTVDATGVTVDIGAVPDSASQLGSSINAGLITIQLSEAYKINHDFTFSGLSKTTDRRLSEVFPITHDGSDGMTPAVIHTRLDGTIVVVEFSTTRSHNIGGLEAAYRTKIEKYRDPISRRVDIMENPRVFFGVIVVSSGGVLSNMPLTQDEAEELMYRFCIANEIYTKARSMDADIELQKSEEELEAISRALSFFSLFEPNIERVEGTFPNSEIKMLEQFLSTPADVDFITKTLKAKEVEAYADLCDSHYLKPEKTIQERLEINRCEAIDKTQDLLAGLHARSNKQTSLNRGTVKLPPWLPKPSSESIDIKTDSGFGSLMDHGAYGELWAKCLLDVSLGNVEGVVSDPAKELDIAISDDPEKDTPKEAKITYRRFKPALSSSARQEFSLQGVEGKKWKRMAANQKKEKESHETLSPFLDVEDIGDFLTFNNLLTDSRYGDESIQRAVSILLEKASAMQDTELTHALNDSFKRNLSSNVVQWSLWVSCLAQELASALKQHCRAGEFIIKKLKFWPIYVIIKPTKSSSHIFYSLGIRKADVTRRLTGRVFSDTIDAGEWELTEFKSLKTCKLTNLVNLPCTMLNSIAFWREKLGVAPWLVRKPCSELREQVGLTFLISLEDKSKTEEIITLTRYTQMEGFVSPPMLPKPQKMLGKLDGPLRTKLQVYLLRKHLDCMVRIASQPFSLIPREGRVEWGGTFHAISGRSTNLENMVNSWYIGYYKNKEESTELNALGEMYKKIVEMEEDKPSSPEFLGWGDTDSPKKHEFSRSFLRAACSSLEREIAQRHGRQWKQNLEERVLREIGTKNILDLASMKATSNFSKDWELYSEVQTKEYHRSKLLEKMATLIEKGVMWYIDAVGQAWKAVLDDGCMRICLFKKNQHGGLREIYVMDANARLVQFGVETMARCVCELSPHETVANPRLKNSIIENHGLKSARSLGPGSININSSNDAKKWNQGHYTTKLALVLCWFMPAKFHRFIWAAISMFRRKKMMVDLRFLAHLSSKSESRSSDPFREAMTDAFHGNRDVSWMDKGRTYIKTETGMMQGILHFTSSLLHSCVQSFYKSYFVSKLKEGYMGESISGVVDVIEGSDDSAIMISIRPKSDMDEVRSRFFVANLLHSVKFLNPLFGIYSSEKSTVNTVYCVEYNSEFHFHRHLVRPTLRWIAASHQISETEALASRQEDYSNLLTQCLEGGASFSLTYLIQCAQLLHHYMLLGLCLHPLFGTFMGMLISDPDPALGFFLMDNPAFAGGAGFRFNLWRACKTTDLGRKYAYYFNEIQGKTKGDEDYRALDATSGGTLSHSVMVYWGDRKKYQALLNRMGLPEDWVEQIDENPGVLYRRAANKKELLLKLAEKVHSPGVTSSLSKGHVVPRVVAAGVYLLSRHCFRFSSSIHGRGSTQKASLIKLLMMSSISAMKHGGSLNPNQERMLFPQAQEYDRVCTLLEEVEHLTGKFVVRERNIVRSRIDLFQEPVDLRCKAEDLVSEVWFGLKRTKLGPRLLKEEWDKLRASFAWLSTDPSETLRDGPFLSHVQFRNFIAHVDAKSRSVRLLGAPVKKSGGVTTISQVVRMNFFPGFSLEAEKSLDNQERLESISILKHVLFMVLNGPYTEEYKLEMIIEAFSTLVIPQPSEVIRKSRTMTLCLLSNYLSSRGGSILDQIERAQSGTLGGFSKPQKTFVRPGGGVGYKGKGVWTGVMEDTHVQILIDGDGTSNWLEEIRLSSDARLYDVIESIRRLCDDLGINNRVASAYRGHCMVRLSGFKIKPASRTDGCPVRIMERGFRIRELQNPDEVKMRVRGDILNLSVTIQEGRVMNILSYRPRDTDISESAAAYLWSNRDLFSFGKKEPSCSWICLKTLDNWAWSHASVLLANDRKTQGIDNRAMGNIFRDCLEGSLRKQGLMRSKLTEMVEKNVVPLTTQELVDILEEDIDFSDVIAVELSEGSLDIESIFDGAPILWSAEVEEFGEGVVAVSYSSKYYHLTLMDQAAITMCAIMGKEGCRGLLTEKRCMAAIREQVRPFLIFLQIPEDSISWVSDQFCDSRGLDEESTIMWG

来源 Source

来源生物 organism	SFTS virus AH12
NCBI 分类编号 ncbi_taxonomy_id	992210
宿主生物 host_organism	Trichoplusia ni

Entity 2 polymer

描述 description	RNA primer
分子量 formula_weight	6452.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	P,E

ACACAGAGACGCCCAGAUGA

Entity 3 polymer

描述 description	;RNA (5'-R(PCPUPGPGPGPCPGPGPUPCPUPUPUPGPUPGP*U)-3') ;
分子量 formula_weight	8386.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	T

AAAAAAGAUCUGGGCGGUCUUUGUGU

Entity 4 polymer

描述 description	RNA primer tail-end
分子量 formula_weight	5094.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	G

AAAACGCAACCAACAC

Entity 5 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (2)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.98 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	67479

fit	/app/data/saxs_computation/r6/8r6u/8r6u.fit
pddf	/app/data/pr_computation/r6/8r6u/8r6u.pr.out
profile	/app/data/saxs_computation/r6/8r6u/8r6u.dat

Structure of the SFTSV L protein in a transcription-priming state without capped RNA [TRANSCRIPTION-PRIMING (in vitro)]

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

冷冻电镜 EM 3D

5. 实体与聚合体信息 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 non-polymer

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)